Basic nitrogen-containing compounds such as pyridine are well known to be inhibitors of the hydrodesulfurization (HDS) reaction for the MoS2-based catalysts. From an interplay of scanning tunneling microscopy (STM) experiments and density functional theory (DFT) calculations, atomic-scale insight into pyridine adsorption on MoS2 is obtained. In agreement with previous IR-spectroscopy and DFT studies, the STM results show that the pyridine molecule itself interacts weakly or not at all with the MoS2 nanoclusters. However, in the presence of hydrogen at the MoS2 edges, adsorbed species are revealed by STM also at the edges. The calculated DFT energies and simulated STM images allowed us to conclude that these species are pyridinium ions located at the catalytically active brim sites. Furthermore, the DFT results for the vibrational modes of the adsorbed pyridinium species agree well with those observed in earlier IR experiments on high surface alumina-supported MoS2 catalyst. The adsorption sites appear to be very similar to the brim sites involved in hydrogenation reactions in HDS. Thus, the combined STM and DFT results provide new atomic-scale insight into the inhibition effect of basic N-compounds in HDS and the first direct observation of the adsorption mode of basic N-compounds on the catalytically active MoS2 edges. Our results lend further support to previously reported correlations between inhibiting strength and proton affinity for the N-containing compounds. (C) 2010 Elsevier Inc. All rights reserved.